diff compnovo.xml @ 2:cf0d72c7b482 draft

Update.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compnovo.xml	Fri May 10 17:31:05 2013 -0400
@@ -0,0 +1,69 @@
+<tool id="compnovo" version="0.1.0" name="CompNovo (OpenMS)">
+  <description>
+    Performs a de novo peptide identification using the CompNovo engine.
+  </description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="stdio" />
+  <expand macro="requires" />
+  <command interpreter="python">
+    #if str($mode) == "cid"
+    #set $executable = "CompNovoCID"
+    #else
+    #set $executable = "CompNovo"
+    #end if
+    openms_wrapper.py --executable '$executable' --config $config
+  </command>
+  <configfiles>
+    <configfile name="config">[simple_options]
+in=${input1}
+out=${out}
+#set $fixed_mods_str=",".join([str($fixed_mod.fixed_mod) for $fixed_mod in $fixed_mods])
+#if $fixed_mods_str
+algorithm!fixed_modifications=$fixed_mods_str
+#end if
+#set $variable_mods_str=",".join([str($variable_mod.fixed_mod) for $variable_mod in $variable_mods])
+#if $variable_mods_str
+algorithm!variable_modifications=$variable_mods_str
+#end if
+</configfile>
+  </configfiles>
+  <inputs>
+    <param name="input1" type="data" format="mzml" label="Input peak list" />
+    <param name="mode" type="select" label="Mode">
+      <option value="cid">CID-only</option>
+      <option value="cidetd">CID/ETD</option>
+    </param>
+    <repeat name="fixed_mods" title="Fixed Modification">
+      <param name="fixed_mod" type="select" label="Fixed Modification">
+        <options from_file="openms_mods.loc">
+          <column name="name" index="0" />
+          <column name="value" index="0" />
+        </options>
+      </param>
+    </repeat>
+    <repeat name="variable_mods" title="Variable Modification">
+      <param name="variable_mod" type="select" label="Variable Modification">
+        <options from_file="openms_mods.loc">
+          <column name="name" index="0"/>
+          <column name="value" index="0" />
+        </options>
+      </param>
+    </repeat>
+  </inputs>
+  <outputs>
+    <data format="idxml" name="out" />
+  </outputs>
+  <help>
+**What it does**
+
+De novo peptide sequencing of mass spectrometry data. 
+
+**Citation**
+
+For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` and ``Bertsch A, Leinenbach A, Pervukhin A, Lubeck M, Hartmer R, Baessmann C, et al.: De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation. Electrophoresis 2009, 30:3736-3747.``
+
+If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
+  </help>
+</tool>